Files in jackolney/CascadeDashboard

A Shiny App for Investigating The Current Trajectory of HIV Care

.Rbuildignore

.travis.yml

DESCRIPTION

NAMESPACE

R/calibration.R R/launch.R R/optimisation.R README.md

_config.yml

appveyor.yml

captures/interpolation-test/local-test.pdf captures/kenya-calibration-weight.pdf captures/kenya-calibration.pdf

captures/optim-barchart-equation.png

captures/thesis.RData

captures/thesis2.RData

captures/weight-test/kenya-amber.pdf captures/weight-test/kenya-green.pdf captures/weight-test/kenya-red.pdf formal/DRC/DRC-analysis.R formal/DRC/DRC-optim.R

formal/DRC/UNAIDS-90-90-90.RData

formal/DRC/combo-fig.R

formal/DRC/data-29-03-17.RData

formal/DRC/fig/cal/CD4-2010.pdf formal/DRC/fig/cal/CD4-2015.pdf formal/DRC/fig/cal/calib-data.pdf formal/DRC/fig/opt/changes.pdf formal/DRC/fig/opt/frontier.pdf formal/DRC/fig/pro/90-90-90-combo.pdf formal/DRC/fig/pro/90-90-90.pdf formal/DRC/fig/pro/AIDS-deaths.pdf formal/DRC/fig/pro/CD4-2020.pdf formal/DRC/fig/pro/cascade-discrete.pdf formal/DRC/fig/pro/cascade-powers.pdf formal/DRC/fig/pro/cascade-projection.pdf formal/DRC/fig/pro/new-infections.pdf formal/UNAIDS/extract-data.R formal/UNAIDS/functions.R

formal/UNAIDS/results/Brazil/Brazil.RData

formal/UNAIDS/results/Brazil/Brazil.xlsx

formal/UNAIDS/results/Brazil/cascade-2015.pdf formal/UNAIDS/results/Brazil/cascade-detail.pdf formal/UNAIDS/results/Brazil/parameter-hist.pdf formal/UNAIDS/results/Brazil/sim-error.pdf

formal/UNAIDS/results/Cambodia/Cambodia.RData

formal/UNAIDS/results/Cambodia/Cambodia.xlsx

formal/UNAIDS/results/Cambodia/cascade-2015.pdf formal/UNAIDS/results/Cambodia/cascade-detail.pdf formal/UNAIDS/results/Cambodia/parameter-hist.pdf formal/UNAIDS/results/Cambodia/sim-error.pdf

formal/UNAIDS/results/Cameroon/Cameroon.RData

formal/UNAIDS/results/Cameroon/Cameroon.xlsx

formal/UNAIDS/results/Cameroon/cascade-2015.pdf formal/UNAIDS/results/Cameroon/cascade-detail.pdf formal/UNAIDS/results/Cameroon/parameter-hist.pdf formal/UNAIDS/results/Cameroon/sim-error.pdf

formal/UNAIDS/results/CotedIvoire/Cote d'Ivoire.RData

formal/UNAIDS/results/CotedIvoire/Cote d'Ivoire.xlsx

formal/UNAIDS/results/CotedIvoire/cascade-2015.pdf formal/UNAIDS/results/CotedIvoire/cascade-detail.pdf formal/UNAIDS/results/CotedIvoire/parameter-hist.pdf formal/UNAIDS/results/CotedIvoire/sim-error.pdf

formal/UNAIDS/results/DRC/DRC.RData

formal/UNAIDS/results/DRC/DRC.xlsx

formal/UNAIDS/results/DRC/cascade-2015.pdf formal/UNAIDS/results/DRC/cascade-detail.pdf formal/UNAIDS/results/DRC/parameter-hist.pdf formal/UNAIDS/results/DRC/sim-error.pdf

formal/UNAIDS/results/Ethiopia/Ethiopia.RData

formal/UNAIDS/results/Ethiopia/Ethiopia.xlsx

formal/UNAIDS/results/Ethiopia/cascade-2015.pdf formal/UNAIDS/results/Ethiopia/cascade-detail.pdf formal/UNAIDS/results/Ethiopia/parameter-hist.pdf formal/UNAIDS/results/Ethiopia/sim-error.pdf

formal/UNAIDS/results/Haiti/Haiti.RData

formal/UNAIDS/results/Haiti/Haiti.xlsx

formal/UNAIDS/results/Haiti/cascade-2015.pdf formal/UNAIDS/results/Haiti/cascade-detail.pdf formal/UNAIDS/results/Haiti/parameter-hist.pdf formal/UNAIDS/results/Haiti/sim-error.pdf

formal/UNAIDS/results/Indonesia/Indonesia.RData

formal/UNAIDS/results/Indonesia/Indonesia.xlsx

formal/UNAIDS/results/Indonesia/cascade-2015.pdf formal/UNAIDS/results/Indonesia/cascade-detail.pdf formal/UNAIDS/results/Indonesia/parameter-hist.pdf formal/UNAIDS/results/Indonesia/sim-error.pdf

formal/UNAIDS/results/Jamaica/Jamaica.RData

formal/UNAIDS/results/Jamaica/Jamaica.xlsx

formal/UNAIDS/results/Jamaica/cascade-2015.pdf formal/UNAIDS/results/Jamaica/cascade-detail.pdf formal/UNAIDS/results/Jamaica/parameter-hist.pdf formal/UNAIDS/results/Jamaica/sim-error.pdf

formal/UNAIDS/results/Kenya/Kenya.RData

formal/UNAIDS/results/Kenya/Kenya.xlsx

formal/UNAIDS/results/Kenya/cascade-2015.pdf formal/UNAIDS/results/Kenya/cascade-detail.pdf formal/UNAIDS/results/Kenya/parameter-hist.pdf formal/UNAIDS/results/Kenya/sim-error.pdf

formal/UNAIDS/results/Malawi/Malawi.RData

formal/UNAIDS/results/Malawi/Malawi.xlsx

formal/UNAIDS/results/Malawi/cascade-2015.pdf formal/UNAIDS/results/Malawi/cascade-detail.pdf formal/UNAIDS/results/Malawi/parameter-hist.pdf formal/UNAIDS/results/Malawi/sim-error.pdf

formal/UNAIDS/results/Morocco/Morocco.RData

formal/UNAIDS/results/Morocco/Morocco.xlsx

formal/UNAIDS/results/Morocco/cascade-2015.pdf formal/UNAIDS/results/Morocco/cascade-detail.pdf formal/UNAIDS/results/Morocco/parameter-hist.pdf formal/UNAIDS/results/Morocco/sim-error.pdf

formal/UNAIDS/results/Mozambique/Mozambique.RData

formal/UNAIDS/results/Mozambique/Mozambique.xlsx

formal/UNAIDS/results/Mozambique/cascade-2015.pdf formal/UNAIDS/results/Mozambique/cascade-detail.pdf formal/UNAIDS/results/Mozambique/parameter-hist.pdf formal/UNAIDS/results/Mozambique/sim-error.pdf

formal/UNAIDS/results/Myanmar/Myanmar.RData

formal/UNAIDS/results/Myanmar/Myanmar.xlsx

formal/UNAIDS/results/Myanmar/cascade-2015.pdf formal/UNAIDS/results/Myanmar/cascade-detail.pdf formal/UNAIDS/results/Myanmar/parameter-hist.pdf formal/UNAIDS/results/Myanmar/sim-error.pdf

formal/UNAIDS/results/Nigeria/Nigeria.RData

formal/UNAIDS/results/Nigeria/Nigeria.xlsx

formal/UNAIDS/results/Nigeria/cascade-2015.pdf formal/UNAIDS/results/Nigeria/cascade-detail.pdf formal/UNAIDS/results/Nigeria/parameter-hist.pdf formal/UNAIDS/results/Nigeria/sim-error.pdf

formal/UNAIDS/results/Pakistan/Pakistan.RData

formal/UNAIDS/results/Pakistan/Pakistan.xlsx

formal/UNAIDS/results/Pakistan/cascade-2015.pdf formal/UNAIDS/results/Pakistan/cascade-detail.pdf formal/UNAIDS/results/Pakistan/parameter-hist.pdf formal/UNAIDS/results/Pakistan/sim-error.pdf

formal/UNAIDS/results/Philippines/Philippines.RData

formal/UNAIDS/results/Philippines/Philippines.xlsx

formal/UNAIDS/results/Philippines/cascade-2015.pdf formal/UNAIDS/results/Philippines/cascade-detail.pdf formal/UNAIDS/results/Philippines/parameter-hist.pdf formal/UNAIDS/results/Philippines/sim-error.pdf

formal/UNAIDS/results/SouthAfrica/South Africa.RData

formal/UNAIDS/results/SouthAfrica/South Africa.xlsx

formal/UNAIDS/results/SouthAfrica/cascade-2015.pdf formal/UNAIDS/results/SouthAfrica/cascade-detail.pdf formal/UNAIDS/results/SouthAfrica/parameter-hist.pdf formal/UNAIDS/results/SouthAfrica/sim-error.pdf

formal/UNAIDS/results/Tanzania/Tanzania.RData

formal/UNAIDS/results/Tanzania/Tanzania.xlsx

formal/UNAIDS/results/Tanzania/cascade-2015.pdf formal/UNAIDS/results/Tanzania/cascade-detail.pdf formal/UNAIDS/results/Tanzania/parameter-hist.pdf formal/UNAIDS/results/Tanzania/sim-error.pdf

formal/UNAIDS/results/Thailand/Thailand.RData

formal/UNAIDS/results/Thailand/Thailand.xlsx

formal/UNAIDS/results/Thailand/cascade-2015.pdf formal/UNAIDS/results/Thailand/cascade-detail.pdf formal/UNAIDS/results/Thailand/parameter-hist.pdf formal/UNAIDS/results/Thailand/sim-error.pdf

formal/UNAIDS/results/Uganda/Uganda.RData

formal/UNAIDS/results/Uganda/Uganda.xlsx

formal/UNAIDS/results/Uganda/cascade-2015.pdf formal/UNAIDS/results/Uganda/cascade-detail.pdf formal/UNAIDS/results/Uganda/parameter-hist.pdf formal/UNAIDS/results/Uganda/sim-error.pdf

formal/UNAIDS/results/Ukraine/Ukraine.RData

formal/UNAIDS/results/Ukraine/Ukraine.xlsx

formal/UNAIDS/results/Ukraine/cascade-2015.pdf formal/UNAIDS/results/Ukraine/cascade-detail.pdf formal/UNAIDS/results/Ukraine/parameter-hist.pdf formal/UNAIDS/results/Ukraine/sim-error.pdf

formal/UNAIDS/results/Vietnam/Vietnam.RData

formal/UNAIDS/results/Vietnam/Vietnam.xlsx

formal/UNAIDS/results/Vietnam/cascade-2015.pdf formal/UNAIDS/results/Vietnam/cascade-detail.pdf formal/UNAIDS/results/Vietnam/parameter-hist.pdf formal/UNAIDS/results/Vietnam/sim-error.pdf

formal/UNAIDS/results/Zimbabwe/Zimbabwe.RData

formal/UNAIDS/results/Zimbabwe/Zimbabwe.xlsx

formal/UNAIDS/results/Zimbabwe/cascade-2015.pdf formal/UNAIDS/results/Zimbabwe/cascade-detail.pdf formal/UNAIDS/results/Zimbabwe/parameter-hist.pdf formal/UNAIDS/results/Zimbabwe/sim-error.pdf

formal/UNAIDS/results/results-figures.docx

formal/UNAIDS/results/results-truncated.xlsx

formal/UNAIDS/results/results.xlsx

formal/initial.R

formal/nigeria/data-28-03-17.RData

formal/nigeria/fig/cal/CD4-2010.pdf formal/nigeria/fig/cal/CD4-2015.pdf formal/nigeria/fig/cal/calib-data.pdf formal/nigeria/fig/cal/calib-detail.pdf formal/nigeria/fig/cal/calib-hist.pdf formal/nigeria/fig/cal/cascade-2015.pdf formal/nigeria/fig/cal/par-hist.pdf formal/nigeria/fig/pro/90-90-90.pdf formal/nigeria/fig/pro/AIDS-deaths.pdf formal/nigeria/fig/pro/cascade-discrete.pdf formal/nigeria/fig/pro/cascade-powers.pdf formal/nigeria/fig/pro/cascade-projection.pdf formal/nigeria/fig/pro/new-infections.pdf formal/nigeria/nigeria-analysis.R formal/nigeria/nigeria-optim.R formal/zimbabwe/PHIA/analysis-CD4-weight.R formal/zimbabwe/PHIA/analysis.R formal/zimbabwe/PHIA/clustr.R

formal/zimbabwe/PHIA/data-24-01-17.RData

formal/zimbabwe/PHIA/data.RData

formal/zimbabwe/PHIA/fig/cal/CD4-2010.pdf formal/zimbabwe/PHIA/fig/cal/CD4-2015.pdf formal/zimbabwe/PHIA/fig/cal/PHIA.pdf formal/zimbabwe/PHIA/fig/cal/calib-data.pdf formal/zimbabwe/PHIA/fig/cal/calib-detail.pdf formal/zimbabwe/PHIA/fig/cal/calib-hist.pdf formal/zimbabwe/PHIA/fig/cal/cascade-2015.pdf formal/zimbabwe/PHIA/fig/cal/par-hist.pdf formal/zimbabwe/PHIA/fig/opt/changes-dodge.pdf formal/zimbabwe/PHIA/fig/opt/changes.pdf formal/zimbabwe/PHIA/fig/opt/frontier.pdf formal/zimbabwe/PHIA/fig/pro/90-90-90.pdf formal/zimbabwe/PHIA/fig/pro/AIDS-deaths.pdf formal/zimbabwe/PHIA/fig/pro/CD4-2015.pdf formal/zimbabwe/PHIA/fig/pro/CD4-2020.pdf formal/zimbabwe/PHIA/fig/pro/cascade-discrete.pdf formal/zimbabwe/PHIA/fig/pro/cascade-powers.pdf formal/zimbabwe/PHIA/fig/pro/cascade-projection.pdf formal/zimbabwe/PHIA/fig/pro/new-infections.pdf formal/zimbabwe/PHIA/optim-CD4-weight.R formal/zimbabwe/PHIA/optim-functions.R formal/zimbabwe/PHIA/optim.R

formal/zimbabwe/UNAIDS-90-90-90.RData

formal/zimbabwe/analysis.R

formal/zimbabwe/big-data.RData

formal/zimbabwe/data.RData

formal/zimbabwe/fig/cal/calib-data-blue.pdf formal/zimbabwe/fig/cal/calib-data-set1.pdf formal/zimbabwe/fig/cal/calib-data.pdf formal/zimbabwe/fig/cal/calib-detail.pdf formal/zimbabwe/fig/cal/calib-hist.pdf formal/zimbabwe/fig/cal/cascade-2015.pdf formal/zimbabwe/fig/cal/par-hist.pdf formal/zimbabwe/fig/opt/changes.pdf formal/zimbabwe/fig/opt/frontier.pdf formal/zimbabwe/fig/pro/90-90-90.pdf formal/zimbabwe/fig/pro/AIDS-deaths.pdf formal/zimbabwe/fig/pro/cascade-discrete.pdf formal/zimbabwe/fig/pro/cascade-powers.pdf formal/zimbabwe/fig/pro/cascade-projection.pdf formal/zimbabwe/fig/pro/new-infections.pdf formal/zimbabwe/post-croatia/analysis.R

formal/zimbabwe/post-croatia/data.RData

formal/zimbabwe/post-croatia/fig/cal/calib-data.pdf formal/zimbabwe/post-croatia/fig/cal/calib-detail.pdf formal/zimbabwe/post-croatia/fig/cal/calib-hist.pdf formal/zimbabwe/post-croatia/fig/cal/cascade-2015.pdf formal/zimbabwe/post-croatia/fig/cal/par-hist.pdf formal/zimbabwe/post-croatia/fig/opt/changes.pdf formal/zimbabwe/post-croatia/fig/opt/frontier.pdf formal/zimbabwe/post-croatia/fig/pro/90-90-90.pdf formal/zimbabwe/post-croatia/fig/pro/AIDS-deaths.pdf formal/zimbabwe/post-croatia/fig/pro/cascade-discrete.pdf formal/zimbabwe/post-croatia/fig/pro/cascade-powers.pdf formal/zimbabwe/post-croatia/fig/pro/cascade-projection.pdf formal/zimbabwe/post-croatia/fig/pro/new-infections.pdf inst/app/clustr-initial.R

inst/app/google-analytics.js

inst/app/rsconnect/shinyapps.io/jackolney/CascadeDashboard.dcf

inst/app/server.R inst/app/server/alert.R inst/app/server/app.R inst/app/server/calibration/advanced-calibration.R inst/app/server/calibration/assumptions.R inst/app/server/calibration/calibration-data.R inst/app/server/calibration/calibration.R inst/app/server/calibration/check-data.R inst/app/server/calibration/confirm-data.R inst/app/server/calibration/data-table.R inst/app/server/calibration/error.R inst/app/server/calibration/initial.R inst/app/server/calibration/marrakech-data.R inst/app/server/calibration/master.R inst/app/server/calibration/misc-functions.R inst/app/server/calibration/mission-control.R inst/app/server/calibration/model.R inst/app/server/calibration/observe-input.R inst/app/server/calibration/observe-output.R inst/app/server/calibration/plot-functions.R inst/app/server/calibration/plot.R inst/app/server/calibration/result.R inst/app/server/calibration/tx-guidelines.R inst/app/server/calibration/update-input.R inst/app/server/country/misc-functions.R inst/app/server/country/observe.R inst/app/server/country/plot-functions.R inst/app/server/country/plot.R inst/app/server/country/rhandsontable.R

inst/app/server/data/calibration/art.csv

inst/app/server/data/calibration/cd4-distribution-2010.csv

inst/app/server/data/calibration/hiv-awareness-unaids.csv

inst/app/server/data/calibration/incidence-uncertainty.csv

inst/app/server/data/calibration/incident-infections.csv

inst/app/server/data/calibration/not-on-art.csv

inst/app/server/data/calibration/plhiv.csv

inst/app/server/data/calibration/previous-data-original.csv

inst/app/server/data/calibration/previous-data.csv

inst/app/server/data/calibration/rates.csv

inst/app/server/data/calibration/thembisa-cascade.csv

inst/app/server/data/calibration/thembisa-incidence.csv

inst/app/server/data/calibration/thembisa-population.csv

inst/app/server/data/calibration/treatment-guidelines-cd4.csv

inst/app/server/data/calibration/treatment-guidelines.csv

inst/app/server/data/leaflet-countries/ne_50m_admin_0_countries.README.html

inst/app/server/data/leaflet-countries/ne_50m_admin_0_countries.VERSION.txt

inst/app/server/data/leaflet-countries/ne_50m_admin_0_countries.dbf

inst/app/server/data/leaflet-countries/ne_50m_admin_0_countries.prj

inst/app/server/data/leaflet-countries/ne_50m_admin_0_countries.shp

inst/app/server/data/leaflet-countries/ne_50m_admin_0_countries.shx

inst/app/server/data/marrakech.csv

inst/app/server/data/projection/cd4-distribution-2015.csv

inst/app/server/data/projection/new-infections-2014.csv

inst/app/server/data/projection/population.csv

inst/app/server/diagnostics.R inst/app/server/file-io.R inst/app/server/font.R inst/app/server/leaflet.R inst/app/server/links.R inst/app/server/misc-functions.R inst/app/server/model/baseline-model.R inst/app/server/model/best-fit-model.R inst/app/server/model/beta.R inst/app/server/model/initial.R inst/app/server/model/model.R inst/app/server/model/parameters.R inst/app/server/model/sim-abs.R inst/app/server/model/sim-prop.R inst/app/server/non-shiny/interpolation-test/cluster-test.R inst/app/server/non-shiny/interpolation-test/local-test.R inst/app/server/non-shiny/interpolation-test/test-function.R inst/app/server/non-shiny/non-shiny-calibration-test.R inst/app/server/non-shiny/non-shiny-calibration.R inst/app/server/non-shiny/non-shiny-optimisation.R inst/app/server/non-shiny/non-shiny-triggers.R inst/app/server/non-shiny/thesis/thesis-figures.R inst/app/server/non-shiny/thesis/thesis.R inst/app/server/optimisation/frontier.R inst/app/server/optimisation/input-functions.R inst/app/server/optimisation/intervention-control.R inst/app/server/optimisation/observe-input.R inst/app/server/optimisation/observe.R inst/app/server/optimisation/optimise.R inst/app/server/optimisation/output-functions.R inst/app/server/optimisation/parameters.R inst/app/server/optimisation/plot-functions.R inst/app/server/optimisation/plot.R inst/app/server/optimisation/prediction.R inst/app/server/optimisation/reactive.R inst/app/server/optimisation/table.R inst/app/server/optimisation/target.R inst/app/server/optimisation/unaids-goal.R inst/app/server/optimisation/update-cost.R inst/app/server/projection/data-table.R inst/app/server/projection/extract-data.R inst/app/server/projection/observe-event.R inst/app/server/projection/plot-functions.R inst/app/server/projection/plot.R inst/app/server/projection/reactive.R inst/app/server/report-fig.R inst/app/server/report.R inst/app/server/report.Rmd inst/app/server/server-head.R inst/app/server/valuebox-baseline.R inst/app/server/valuebox.R inst/app/server/vars.R

inst/app/styles.css

inst/app/tests/src/calibration.R inst/app/tests/src/optimisation.R inst/app/tests/test-1-data.R inst/app/tests/test-2-calibration.R inst/app/tests/test-3-projection.R inst/app/tests/test-4-optimisation.R inst/app/ui.R inst/app/ui/dashboardheader.R inst/app/ui/global-lists.R inst/app/ui/introduction.R inst/app/ui/more/more_allplot.R inst/app/ui/more/more_modeldocument.R inst/app/ui/more/more_report.R inst/app/ui/more/more_singleplot.R inst/app/ui/more/session.R inst/app/ui/optimisation/opt-909090.R inst/app/ui/optimisation/opt-best-fit.R inst/app/ui/optimisation/opt-cost.R inst/app/ui/optimisation/opt-intro.R inst/app/ui/optimisation/opt-parameter.R inst/app/ui/results/res_909090.R inst/app/ui/results/res_carecascade.R inst/app/ui/results/res_incidence.R inst/app/ui/results/res_mortality.R inst/app/ui/results/res_powerscascade.R inst/app/ui/results/res_yourcascade.R inst/app/ui/setup/calibration.R inst/app/ui/setup/country.R inst/app/ui/setup/data-review.R inst/app/ui/setup/diagnosis.R inst/app/ui/setup/edit-country/edit-cascade.R inst/app/ui/setup/edit-country/edit-cd4.R inst/app/ui/setup/edit-country/edit-guidelines.R inst/app/ui/setup/edit-country/edit-incidence.R inst/app/ui/setup/linkage.R inst/app/ui/setup/parameters.R inst/app/ui/setup/plhiv.R inst/app/ui/setup/suppression.R inst/app/ui/setup/treatment.R inst/app/ui/sidebar.R inst/app/ui/uihead.R

inst/app/www/HIVMC-logo.jpg

inst/app/www/Model.png

inst/app/www/ModelSimple.png

inst/app/www/WHO-Guidelines-Front-Crop.png

inst/app/www/WHO-Guidelines-Front.png

inst/app/www/WHOGuidelinesCascade.png

inst/app/www/hivmc-icon.png

inst/app/www/report-sample.png

inst/app/www/si-indicators/aids-deaths.png

inst/app/www/si-indicators/art.png

inst/app/www/si-indicators/diagnosed.png

inst/app/www/si-indicators/linkage.png

inst/app/www/si-indicators/new-infections.png

inst/app/www/si-indicators/plhiv.png

inst/app/www/si-indicators/retention.png

inst/app/www/si-indicators/suppression.png

man/RunClusterCalibration.Rd man/RunClusterOptimisation.Rd man/launch.Rd tests/testthat.R tests/testthat/src/calibration.R tests/testthat/src/optimisation.R tests/testthat/test-1-data.R tests/testthat/test-2-calibration.R tests/testthat/test-3-projection.R tests/testthat/test-4-optimisation.R

jackolney/CascadeDashboard documentation built on May 18, 2019, 7:56 a.m.